LAMMPS (27 Oct 2021)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
# LAMMPS input file for 26.5% benzene mole fraction solution
# with 380 benzene and 1000 water molecules,
# using all possible local density potentials
# between benzene and water
#
# Author: Tanmoy Sanyal, Shell Group, UC Santa Barbara
#
# Refer: Sanyal and Shell, JPC-B, 2018, 122 (21), 5678-5693



# Initialize simulation box
dimension       3
boundary        p p p
units           real
atom_style      molecular

# Set potential styles
pair_style      hybrid/overlay table spline 500 local/density

# Read molecule data and set initial velocities
read_data       benzene_water.data
Reading data file ...
  orthogonal box = (-12.865000 -12.865000 -64.829000) to (12.865000 12.865000 64.829000)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  1380 atoms
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     0 = max # of 1-2 neighbors
     0 = max # of 1-3 neighbors
     0 = max # of 1-4 neighbors
     1 = max # of special neighbors
  special bonds CPU = 0.000 seconds
  read_data CPU = 0.006 seconds
velocity        all create  3.0000e+02 16611 rot yes dist gaussian

# Assign potentials
pair_coeff          1     1    table          benzene_water.pair.table      PairBB
WARNING: 33 of 500 force values in table PairBB are inconsistent with -dE/dr.
WARNING:  Should only be flagged at inflection points (src/pair_table.cpp:465)
WARNING: 150 of 500 distance values in table 1e-06 with relative error
WARNING:  over PairBB to re-computed values (src/pair_table.cpp:473)
pair_coeff          1     2    table          benzene_water.pair.table      PairWW
WARNING: 61 of 500 force values in table PairWW are inconsistent with -dE/dr.
WARNING:  Should only be flagged at inflection points (src/pair_table.cpp:465)
WARNING: 90 of 500 distance values in table 1e-06 with relative error
WARNING:  over PairWW to re-computed values (src/pair_table.cpp:473)
pair_coeff          2     2    table          benzene_water.pair.table      PairBW
WARNING: 108 of 500 force values in table PairBW are inconsistent with -dE/dr.
WARNING:  Should only be flagged at inflection points (src/pair_table.cpp:465)
WARNING: 135 of 500 distance values in table 1e-06 with relative error
WARNING:  over PairBW to re-computed values (src/pair_table.cpp:473)
pair_coeff          *     *    local/density  benzene_water.localdensity.table

# Recentering during minimization and equilibration
fix recentering all recenter 0.0 0.0 0.0 units box

# Thermostat & time integration
timestep        2.0
thermo          100
thermo_style    custom temp ke pe etotal ebond eangle edihed evdwl

# Minimization
minimize        1.e-4 0.0 10000 10000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- pair_style  local/density  command:

@Article{Sanyal16,
 author =  {T.Sanyal and M.Scott Shell},
 title =   {Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation},
 journal = {J.~Chem.~Phys.},
 year =    2016,
 DOI = doi.org/10.1063/1.4958629}

@Article{Sanyal18,
 author =  {T.Sanyal and M.Scott Shell},
 title =   {Transferable coarse-grained models of liquid-liquid equilibrium using local density potentials optimized with the relative entropy},
 journal = {J.~Phys.~Chem. B},
 year =    2018,
 DOI = doi.org/10.1021/acs.jpcb.7b12446}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187)
  generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 15.25
  ghost atom cutoff = 15.25
  binsize = 7.625, bins = 4 4 18
  2 neighbor lists, perpetual/occasional/extra = 2 0 0
  (1) pair table, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
  (2) pair local/density, perpetual, copy from (1)
      attributes: half, newton on
      pair build: copy
      stencil: none
      bin: none
Per MPI rank memory allocation (min/avg/max) = 8.754 | 8.754 | 8.754 Mbytes
Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl 
         300    1233.1611    2374.6749     3607.836            0            0            0    2374.6749 
         300    1233.1611    985.54829    2218.7094            0            0            0    985.54829 
         300    1233.1611    962.66036    2195.8215            0            0            0    962.66036 
Loop time of 0.812343 on 1 procs for 134 steps with 1380 atoms

99.8% CPU use with 1 MPI tasks x 1 OpenMP threads

Minimization stats:
  Stopping criterion = energy tolerance
  Energy initial, next-to-last, final = 
      2374.67491482358   962.664796664787   962.660357218268
  Force two-norm initial, final = 263.77519 15.741017
  Force max component initial, final = 22.412654 7.9360139
  Final line search alpha, max atom move = 0.014975513 0.11884588
  Iterations, force evaluations = 134 240

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.78539    | 0.78539    | 0.78539    |   0.0 | 96.68
Bond    | 2.0149e-05 | 2.0149e-05 | 2.0149e-05 |   0.0 |  0.00
Neigh   | 0.016759   | 0.016759   | 0.016759   |   0.0 |  2.06
Comm    | 0.0045     | 0.0045     | 0.0045     |   0.0 |  0.55
Output  | 2.9402e-05 | 2.9402e-05 | 2.9402e-05 |   0.0 |  0.00
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 0.005647   |            |       |  0.70

Nlocal:        1380.00 ave        1380 max        1380 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:        5832.00 ave        5832 max        5832 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:        78165.0 ave       78165 max       78165 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 78165
Ave neighs/atom = 56.641304
Ave special neighs/atom = 0.0000000
Neighbor list builds = 5
Dangerous builds = 0

# Set up integration parameters
fix             timeintegration all nve
fix             thermostat all langevin  3.0000e+02  3.0000e+02  1.0000e+02 81890

# Equilibration (for realistic results, run for 5000000 steps)
reset_timestep  0
run             5000
  generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
WARNING: Fix recenter should come after all other integration fixes (src/fix_recenter.cpp:133)
Per MPI rank memory allocation (min/avg/max) = 7.629 | 7.629 | 7.629 Mbytes
Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl 
         300    1233.1611    962.66036    2195.8215            0            0            0    962.66036 
    253.1913    1040.7522     1803.711    2844.4633            0            0            0     1803.711 
   290.31049     1193.332    2059.0637    3252.3958            0            0            0    2059.0637 
   299.30778    1230.3157     2140.226    3370.5417            0            0            0     2140.226 
   309.81524     1273.507    2178.3782    3451.8853            0            0            0    2178.3782 
   299.79526    1232.3195    2229.9248    3462.2444            0            0            0    2229.9248 
   299.24909    1230.0745    2260.7129    3490.7874            0            0            0    2260.7129 
    299.5898     1231.475    2244.2384    3475.7134            0            0            0    2244.2384 
   297.81223    1224.1682      2320.27    3544.4382            0            0            0      2320.27 
   301.53975    1239.4903    2277.0431    3516.5334            0            0            0    2277.0431 
   292.00572    1200.3003    2292.3073    3492.6076            0            0            0    2292.3073 
   309.19709    1270.9661    2303.6055    3574.5716            0            0            0    2303.6055 
   297.54933    1223.0876     2304.127    3527.2146            0            0            0     2304.127 
   303.48106    1247.4702    2303.5673    3551.0375            0            0            0    2303.5673 
   296.46047    1218.6118    2256.1591    3474.7709            0            0            0    2256.1591 
    299.4835     1231.038    2280.0452    3511.0832            0            0            0    2280.0452 
   306.25958    1258.8914    2307.9795    3566.8709            0            0            0    2307.9795 
   304.67335    1252.3711    2284.8252    3537.1963            0            0            0    2284.8252 
   298.33637    1226.3227    2289.8499    3516.1726            0            0            0    2289.8499 
    303.1338    1246.0427    2342.2148    3588.2575            0            0            0    2342.2148 
   305.86051     1257.251    2341.0106    3598.2616            0            0            0    2341.0106 
   297.75418    1223.9296    2303.5613    3527.4909            0            0            0    2303.5613 
   296.79348    1219.9806    2327.5207    3547.5013            0            0            0    2327.5207 
   307.25403    1262.9791    2288.4219     3551.401            0            0            0    2288.4219 
   301.26976    1238.3805    2291.2465     3529.627            0            0            0    2291.2465 
   297.17249    1221.5385    2283.3926    3504.9311            0            0            0    2283.3926 
   313.99072    1290.6705    2293.9661    3584.6366            0            0            0    2293.9661 
   301.70804    1240.1821    2331.1694    3571.3515            0            0            0    2331.1694 
   300.62599    1235.7343    2325.4367     3561.171            0            0            0    2325.4367 
   292.13495    1200.8316     2315.631    3516.4626            0            0            0     2315.631 
    313.9981    1290.7008    2286.0536    3576.7545            0            0            0    2286.0536 
   300.25311    1234.2015    2324.2379    3558.4394            0            0            0    2324.2379 
    309.3746    1271.6958    2322.2298    3593.9256            0            0            0    2322.2298 
   300.23041    1234.1082    2332.7521    3566.8603            0            0            0    2332.7521 
   302.97054    1245.3716    2303.1689    3548.5405            0            0            0    2303.1689 
   294.77155    1211.6694    2334.5087    3546.1781            0            0            0    2334.5087 
   296.81476    1220.0681    2322.5932    3542.6613            0            0            0    2322.5932 
   301.83238    1240.6932    2345.4841    3586.1773            0            0            0    2345.4841 
    295.0399    1212.7724    2312.3889    3525.1614            0            0            0    2312.3889 
   300.73565     1236.185    2338.8384    3575.0235            0            0            0    2338.8384 
   303.02264    1245.5858    2310.0868    3555.6726            0            0            0    2310.0868 
   302.86404    1244.9339    2332.2001     3577.134            0            0            0    2332.2001 
   293.77916    1207.5901    2293.2799    3500.8701            0            0            0    2293.2799 
   299.30072    1230.2867    2317.5065    3547.7933            0            0            0    2317.5065 
   311.05029    1278.5837    2311.0476    3589.6313            0            0            0    2311.0476 
   293.25646    1205.4416    2314.7398    3520.1814            0            0            0    2314.7398 
   310.49018    1276.2814    2337.4909    3613.7723            0            0            0    2337.4909 
   302.37336    1242.9169    2340.3197    3583.2366            0            0            0    2340.3197 
   297.06862    1221.1116    2323.9136    3545.0252            0            0            0    2323.9136 
   300.54817    1235.4144    2315.2405    3550.6549            0            0            0    2315.2405 
   309.10643    1270.5934    2333.1848    3603.7783            0            0            0    2333.1848 
Loop time of 15.2696 on 1 procs for 5000 steps with 1380 atoms

Performance: 56.583 ns/day, 0.424 hours/ns, 327.447 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 14.432     | 14.432     | 14.432     |   0.0 | 94.51
Bond    | 0.00032375 | 0.00032375 | 0.00032375 |   0.0 |  0.00
Neigh   | 0.41541    | 0.41541    | 0.41541    |   0.0 |  2.72
Comm    | 0.0975     | 0.0975     | 0.0975     |   0.0 |  0.64
Output  | 0.0013044  | 0.0013044  | 0.0013044  |   0.0 |  0.01
Modify  | 0.30336    | 0.30336    | 0.30336    |   0.0 |  1.99
Other   |            | 0.01973    |            |       |  0.13

Nlocal:        1380.00 ave        1380 max        1380 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:        5843.00 ave        5843 max        5843 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:        76949.0 ave       76949 max       76949 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 76949
Ave neighs/atom = 55.760145
Ave special neighs/atom = 0.0000000
Neighbor list builds = 121
Dangerous builds = 1

# Turn off recentering during production phase
unfix recentering

# Setup trajectory output
dump            myDump all custom 100 benzene_water.lammpstrj.gz id type x y z element
dump_modify     myDump element B W
dump_modify     myDump sort id

# Production (for realistic results, run for 10000000 steps)
reset_timestep  0
run             1000
  generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 9.022 | 9.022 | 9.022 Mbytes
Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl 
   309.10643    1270.5934    2333.1848    3603.7783            0            0            0    2333.1848 
   300.84572    1236.6375    2331.3493    3567.9868            0            0            0    2331.3493 
   300.90599    1236.8852    2337.6775    3574.5627            0            0            0    2337.6775 
   302.77895    1244.5841    2341.7778     3586.362            0            0            0    2341.7778 
   291.66639    1198.9055    2320.3512    3519.2567            0            0            0    2320.3512 
    298.7003    1227.8187    2292.8195    3520.6382            0            0            0    2292.8195 
   301.11163    1237.7305     2310.017    3547.7475            0            0            0     2310.017 
   305.22515    1254.6393    2315.1355    3569.7748            0            0            0    2315.1355 
   295.15921    1213.2629     2310.184    3523.4468            0            0            0     2310.184 
    299.2024    1229.8826    2332.2118    3562.0943            0            0            0    2332.2118 
   302.80078    1244.6738    2320.3763    3565.0502            0            0            0    2320.3763 
Loop time of 3.07208 on 1 procs for 1000 steps with 1380 atoms

Performance: 56.249 ns/day, 0.427 hours/ns, 325.512 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 2.8993     | 2.8993     | 2.8993     |   0.0 | 94.37
Bond    | 6.5327e-05 | 6.5327e-05 | 6.5327e-05 |   0.0 |  0.00
Neigh   | 0.083502   | 0.083502   | 0.083502   |   0.0 |  2.72
Comm    | 0.019967   | 0.019967   | 0.019967   |   0.0 |  0.65
Output  | 0.012268   | 0.012268   | 0.012268   |   0.0 |  0.40
Modify  | 0.052801   | 0.052801   | 0.052801   |   0.0 |  1.72
Other   |            | 0.004203   |            |       |  0.14

Nlocal:        1380.00 ave        1380 max        1380 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:        5860.00 ave        5860 max        5860 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:        77055.0 ave       77055 max       77055 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 77055
Ave neighs/atom = 55.836957
Ave special neighs/atom = 0.0000000
Neighbor list builds = 24
Dangerous builds = 0


Total wall time: 0:00:19
